Self-organisation.
LD cloud grew, nobody designed it.
Knowledge follows power curve. This has an impact on mapping and reasoning, storage and indexing.

Distribution.
Web not geared for distributed SPARQL queries. Everyone pulls in all data and queries local copy. Not very 'webby', disadvantageous. So subgraphs? Query planning? Caching? Payload priority?

Provenance.
Representation, (re)construction. Metametadata (knowledge about knowledge; uncertainty; problems with vocabs for this).
How to get from provenance to trust.